The fishing practices in the oligotrophic Lake Toya, Hokkaido, Japan, have profound implications in the ecosystem sustainability. The status of the sockeye salmon ( Oncorhynchus nerka) population has become a serious concern among the lake managers and policy makers during the last decades. While the decline of the sockeye salmon population has been well documented in Lake Toya, there is considerable uncertainty with regards to the impact on the broader system dynamics. In this study, our objective is to address this knowledge gap by undertaking a synthesis of the Lake Toya food web using the mass-balance modeling software Ecopath with Ecosim ( EwE). Our primary research question is to examine the repercussions of the declining sockeye salmon population on the trophic dynamics of the lake. Namely, we assess if there are any competing species that might have benefited from the decrease of sockeye salmon standing biomass and to what extent do these changes propagate through the Lake Toya food web? Our analysis pinpoints the critical role of the Japanese smelt ( Hypomesus transpacificus nipponensis) in the system, which demonstrates a wide range of effects on several functional groups at both higher and lower trophic levels in Lake Toya. In particular, being a substantial portion of the masu salmon ( Oncorhynchus masou) and adult sockeye salmon diets, the Japanese smelt has a positive impact on the top predators of the system. Amphipods, insects, and shrimp strongly benefit from the autochthonous and allochthonous organic matter in the system, while the tight coupling between phytoplankton and zooplankton seems to be particularly critical for the integrity of the Lake Toya food web. Whereas the values of the different ecosystem attributes (e.g., primary production/biomass, biomass/total throughput, system omnivory index, amount of recycled throughput, Finn's cycling index) provide evidence that Lake Toya is an immature system, we note that the internal redundancy and the system overhead estimates suggest that the lake possesses substantial reserves to overcome external perturbations. We also examined the effects of a variety of fishing policies on the biomass of masu salmon and adult sockeye salmon, which verify the belief that the adult sockeye population is quite fragile with high likelihood to collapse. Our analysis also predicts that sockeye will not rebound unless the fishing pressure exerted is substantially reduced (>50% of the reference levels used). Masu salmon seems to benefit under all the scenarios examined indicating that the intensity of the current fishing activities is significantly lower than its biomass accumulation rate in the system.